Main Results
Cupcake Collapse - Discarded
As expected, all the transcripts discarded in 95% coverage dataset are within the 99% coverage dataset
Numbers
<<<<<<< HEAD <<<<<<< HEADnum <- bind_rows(sapply(c99, nrow) %>% melt() %>% rownames_to_column(., var = "fileinput") %>% mutate(type = "coverage_99"),
sapply(c95, nrow) %>% melt() %>% rownames_to_column(., var = "fileinput") %>% mutate(type = "coverage_95"),
sapply(c85, nrow) %>% melt() %>% rownames_to_column(., var = "fileinput") %>% mutate(type = "coverage_85"))
num %>% filter(fileinput == "cup_coll_ign") %>%
ggplot(., aes(x = fileinput, y = value, fill = type)) + geom_bar(stat = "identity", position = position_dodge()) +
labs(y = "Number of Transcripts Discarded", x = "") + mytheme +
scale_x_discrete(labels=c("Cupcake Collapse")) +
scale_fill_discrete(labels = c("85% Coverage","95% Coverage","99% Coverage"), name = "")Overlap
# intentional mislabelling due to misleading labelling from venn diagram otherwise
grid.draw(venn_diagram_plot_threecircles(c95$cup_coll_ign$V1,c85$cup_coll_ign$V1,c99$cup_coll_ign$V1,"99% Coverage","85% Coverage","95% Coverage"))num <- bind_rows(sapply(c99, nrow) %>% melt() %>% rownames_to_column(., var = "fileinput") %>% mutate(type = "coverage_99"),
sapply(c95, nrow) %>% melt() %>% rownames_to_column(., var = "fileinput") %>% mutate(type = "coverage_95"))
num %>% filter(fileinput == "cup_coll_ign") %>%
ggplot(., aes(x = fileinput, y = value, fill = type)) + geom_bar(stat = "identity", position = position_dodge()) +
labs(y = "Number of Transcripts Discarded", x = "") + mytheme +
scale_x_discrete(labels=c("Cupcake Collapse")) +
scale_fill_discrete(labels = c("95% Coverage","99% Coverage"), name = "")Overlap
Number of unique isoforms
<<<<<<< HEAD <<<<<<< HEAD'%ni%' <- Negate('%in%')
df <- num[num$fileinput %ni% c("cup_coll_ign","sq_ign","sq_tama_discard","sq_tama_id"),]
ggplot(df, aes(x = fileinput, y = value, fill = type)) +
geom_bar(stat = "identity", position = position_dodge()) +
labs(y = "Number of Isoforms", x = "") + mytheme +
scale_x_discrete(labels=c("Cupcake Collapse","Cupcake Filter","Sqanti","Sqanti Filter","Post Tama")) +
scale_fill_discrete(labels = c("85% Coverage", "95% Coverage","99% Coverage"), name = "") +
theme(axis.text.x = element_text(angle = 45, hjust=1))'%ni%' <- Negate('%in%')
df <- num[num$fileinput %ni% c("cup_coll_ign","sq_ign","sq_tama_discard","sq_tama_id"),]
ggplot(df, aes(x = fileinput, y = value, fill = type)) +
geom_bar(stat = "identity", position = position_dodge()) +
labs(y = "Number of Isoforms", x = "") + mytheme +
scale_x_discrete(labels=c("Cupcake Collapse","Cupcake Filter","Sqanti","Sqanti Filter","Post Tama")) +
scale_fill_discrete(labels = c("95% Coverage","99% Coverage"), name = "") +
theme(axis.text.x = element_text(angle = 45, hjust=1))